In [4]:
####
suppressMessages(library(ArchR))
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
suppressMessages(library(Seurat))
suppressMessages(library(SingleCellExperiment))
In [5]:
##################################
### set Arrow File parameters ####
addArchRThreads(threads = 12)
##################################
### load rheMac10 ArchR genome ###
GENOMEDIR='/home/bnphan/resources/genomes/rn7'
load(file.path(GENOMEDIR,'rn7_liftoff_mm10NcbiRefSeq_ArchR_annotations.rda'))
Setting default number of Parallel threads to 12.
In [6]:
PROJDIR='../../../data/tidy_data/ArchRProjects'
ARCHDIR=file.path(PROJDIR,'Rat_Transgen_NAc_scATAC_MSN')
proj = loadArchRProject(ARCHDIR)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
In [7]:
proj <- addImputeWeights(proj, reducedDims = "HarmonyX300")
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-25b9337307ede-Date-2022-12-05_Time-08-48-30.log If there is an issue, please report to github with logFile! 2022-12-05 08:48:30 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
In [8]:
p1 <- plotEmbedding( proj, colorBy = "cellColData", name = "Sample", embedding = "UMAPX300")
p2 <- plotEmbedding( proj, colorBy = "cellColData", name = "Sire", embedding = "UMAPX300")
p3 <- plotEmbedding( proj, colorBy = "cellColData", name = "ClustersX300", embedding = "UMAPX300")
ggAlignPlots(p3,p1, type = "h")
ggAlignPlots(p3,p2, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b935f5e9a66-Date-2022-12-05_Time-08-49-07.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b935f5e9a66-Date-2022-12-05_Time-08-49-07.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b932cf584e7-Date-2022-12-05_Time-08-49-08.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b932cf584e7-Date-2022-12-05_Time-08-49-08.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b93506d7a10-Date-2022-12-05_Time-08-49-08.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b93506d7a10-Date-2022-12-05_Time-08-49-08.log
In [9]:
## make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersX300", embedding = "UMAPX300")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAPX300")
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "nFrags", embedding = "UMAPX300")
ggAlignPlots(p1, p2, p3,type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9383190ff-Date-2022-12-05_Time-08-49-19.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9383190ff-Date-2022-12-05_Time-08-49-19.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9330d37c8f-Date-2022-12-05_Time-08-49-20.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Warning message: “package ‘hexbin’ was built under R version 4.1.3” ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9330d37c8f-Date-2022-12-05_Time-08-49-20.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9362a10c5b-Date-2022-12-05_Time-08-49-21.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9362a10c5b-Date-2022-12-05_Time-08-49-21.log
In [10]:
# Broad MSN marker, mouse 3000600C02Rik == human KIAA1211L
# MSN markers, Ppp1r1b = DARPP-32, Bcl11b=Ctip2
markMSN3 = c('Ppp1r1b', 'Bcl11b', 'Drd1','Drd2','Drd3', 'Cpne4','Rxfp1', 'Lhx6', 'Sst', 'Pthlh')
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN3, embedding = "UMAPX300", imputeWeights = NULL)
p3 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p3))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9321ef15ca-Date-2022-12-05_Time-08-49-26.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 08:49:27 : Plotting Embedding 1 2 3 4 5 6 7 8 9 10 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9321ef15ca-Date-2022-12-05_Time-08-49-26.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [11]:
markMSN1 = c('Drd1','Tac1','Foxp2','Pdyn', 'Cpne4', 'Rxfp1') # D1 markers
# D1 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN1, embedding = "UMAPX300", imputeWeights = NULL) #
p1 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) +
theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p1))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b933e725ece-Date-2022-12-05_Time-08-50-03.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 08:50:03 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b933e725ece-Date-2022-12-05_Time-08-50-03.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [12]:
markMSN2 = c('Drd2','Adora2a','Penk', 'Grik3', 'Sp9', 'Gpr52')# D2 markers
# D2 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markMSN2, embedding = "UMAPX300", imputeWeights = NULL)
p2 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p2))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b93377146ca-Date-2022-12-05_Time-08-50-24.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 08:50:25 : Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b93377146ca-Date-2022-12-05_Time-08-50-24.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [13]:
markFig1 = c('Drd1', 'Drd2', 'Stxbp6', 'Fam163a', 'Gria4', 'Cpne4', 'Rxfp1', 'Casz1')
# D2 MSN
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markFig1, embedding = "UMAPX300", imputeWeights = NULL)
p2 <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(nrow = 2),p2))
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b934fb913d4-Date-2022-12-05_Time-08-50-41.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-12-05 08:50:42 : Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b934fb913d4-Date-2022-12-05_Time-08-50-41.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [14]:
p1 <- plotEmbedding( proj, colorBy = "cellColData", name = "cluster_rat", embedding = "UMAPX300")
p3 <- plotEmbedding( proj, colorBy = "cellColData", name = "ClustersX300", embedding = "UMAPX300")
ggAlignPlots(p3,p1, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9352e34e70-Date-2022-12-05_Time-08-51-04.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9352e34e70-Date-2022-12-05_Time-08-51-04.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9356230cc8-Date-2022-12-05_Time-08-51-05.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9356230cc8-Date-2022-12-05_Time-08-51-05.log
Integrate with snRNA-seq subclusters of MSNs¶
In [15]:
file_sce=here::here('data/tidy_data/HeKleyman2021_macaque_striatum_data_processing',
'rdas/GSE167920_Results_MSNs_processed_final_NAc.mmGenes.sce.rds')
rna_sce = readRDS(file_sce)
In [16]:
head(colData(rna_sce))
table(colData(rna_sce)$MSN_type)
logcounts(rna_sce) = NULL
DataFrame with 6 rows and 9 columns
nCount_RNA nFeature_RNA nCount_SCT nFeature_SCT
<numeric> <integer> <numeric> <integer>
GTGGTTAAGCTTCGTA-1 4635 2317 8611 2450
ATCGCCTGTTGAGGAC-1 6080 2501 8742 2520
CTGATCCAGGTCATTC-7 11201 3672 9887 3670
TCAAGTGTCTATCGGA-7 12590 3844 9973 3823
ATTCTTGCATGGAAGC-4 5007 2379 8641 2468
TCTGGCTGTTCTCTAT-7 16807 4160 9870 3841
integrated_snn_res.0.3 MSN_type region_name monkey
<character> <character> <character> <character>
GTGGTTAAGCTTCGTA-1 0 D1-Matrix nacc Monkey_P
ATCGCCTGTTGAGGAC-1 0 D1-Matrix nacc Monkey_P
CTGATCCAGGTCATTC-7 0 D1-Matrix nacc Monkey_P
TCAAGTGTCTATCGGA-7 0 D1-Matrix nacc Monkey_P
ATTCTTGCATGGAAGC-4 0 D1-Matrix nacc Monkey_P
TCTGGCTGTTCTCTAT-7 0 D1-Matrix nacc Monkey_P
ident
<factor>
GTGGTTAAGCTTCGTA-1 Monkey_P
ATCGCCTGTTGAGGAC-1 Monkey_P
CTGATCCAGGTCATTC-7 Monkey_P
TCAAGTGTCTATCGGA-7 Monkey_P
ATTCTTGCATGGAAGC-4 Monkey_P
TCTGGCTGTTCTCTAT-7 Monkey_P
D1-ICj D1-Matrix D1-NUDAP D1-Shell/OT D1-Striosome D1/D2-Hybrid
185 535 184 518 79 58
D2-Matrix D2-Shell/OT D2-Striosome
590 392 88
In [17]:
#####################################
# integration split by Region region
proj <- addGeneIntegrationMatrix(
ArchRProj = proj,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix",
reducedDims = "HarmonyX300",
seRNA = rna_sce, nGenes = 3000,
addToArrow = FALSE, plotUMAP = TRUE,
groupRNA = "MSN_type",
nameCell = "predictedCell_Co",
nameGroup = "predictedGroup_Co",
nameScore = "predictedScore_Co"
)
ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-25b93394d07ba-Date-2022-12-05_Time-08-51-14.log If there is an issue, please report to github with logFile! 2022-12-05 08:51:14 : Running Seurat's Integration Stuart* et al 2019, 0.002 mins elapsed. 2022-12-05 08:51:15 : Checking ATAC Input, 0.007 mins elapsed. 2022-12-05 08:51:15 : Checking RNA Input, 0.017 mins elapsed. 2022-12-05 08:51:17 : Found 13880 overlapping gene names from gene scores and rna matrix!, 0.055 mins elapsed. 2022-12-05 08:51:17 : Creating Integration Blocks, 0.055 mins elapsed. 2022-12-05 08:51:17 : Prepping Interation Data, 0.056 mins elapsed. 2022-12-05 08:51:19 : Computing Integration in 2 Integration Blocks!, 0 mins elapsed. 2022-12-05 08:57:26 : Block (1 of 2) : Plotting Joint UMAP, 6.115 mins elapsed. 2022-12-05 08:57:56 : Block (2 of 2) : Plotting Joint UMAP, 6.615 mins elapsed. 2022-12-05 08:58:24 : Completed Integration with RNA Matrix, 7.087 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-addGeneIntegrationMatrix-25b93394d07ba-Date-2022-12-05_Time-08-51-14.log
Compare snATAC clusters w/ snRNA clusters¶
In [18]:
# plot the confusion matrix of cell types by predicted cell type clusters
cM <- confusionMatrix(paste0(proj$ClustersX300), paste0(proj$predictedGroup_Co))
cM <- cM / Matrix::rowSums(cM)
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
preClust <- colnames(cM)[apply(cM, 1 , which.max)]
cbind(preClust, rownames(cM)) #Assignments
| preClust | |
|---|---|
| D1-Shell/OT | C8 |
| D2-Shell/OT | C4 |
| D2-Matrix | C13 |
| D2-Matrix | C14 |
| D2-Matrix | C9 |
| D2-Matrix | C11 |
| D2-Matrix | C10 |
| D2-Matrix | C12 |
| D1/D2-Hybrid | C5 |
| D1/D2-Hybrid | C6 |
| D2-Matrix | C7 |
| D1-NUDAP | C1 |
| D1-ICj | C2 |
| D1-ICj | C3 |
In [19]:
p2 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_Co", embedding = "UMAPX300")
p3 <- plotEmbedding( proj, colorBy = "cellColData", name = "cluster_macaque", embedding = "UMAPX300")
ggAlignPlots(p3, p2, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b937693884a-Date-2022-12-05_Time-08-58-25.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b937693884a-Date-2022-12-05_Time-08-58-25.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b932239e16b-Date-2022-12-05_Time-08-58-25.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b932239e16b-Date-2022-12-05_Time-08-58-25.log
Relabel cluster and call peaks¶
In [20]:
############################################
# using marker gene scores, give cluster names
remapClust = c(
'C1' = 'D1-NUDAP-MSN',
'C2' = 'D1-ICj-MSN',
'C3' = 'D1-ICj-MSN',
'C4' = 'Drop',
'C5' = 'D1/D2-Hybrid-MSN',
'C6' = 'D2-MSN',
'C7' = 'Drop',
'C8' = 'Drop',
'C9' = 'Drop',
'C10' = 'Drop',
'C11' = 'Drop',
'C12' = 'Drop',
'C13' = 'Drop',
'C14' = 'Drop')
In [21]:
## perform relabelling
proj$cluster_rat_RNA2ATAC = mapLabels(proj$ClustersX300, newLabels = remapClust, oldLabels = names(remapClust))
## drop cells that aren't confidently mapped to a cell subtype
proj$cluster_rat_RNA2ATAC = ifelse(proj$cluster_rat_RNA2ATAC == 'Drop' &
!is.na(proj$cluster_rat) & grepl('^D', proj$cluster_rat),
proj$cluster_rat, proj$cluster_rat_RNA2ATAC)
table(proj$cluster_rat_RNA2ATAC)
D1-ICj-MSN D1-MSN D1-NUDAP-MSN D1/D2-Hybrid-MSN
617 2172 874 1265
D1/D3-MSN D2-MSN Drop
863 2645 8973
In [22]:
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "cluster_rat", embedding = "UMAPX300")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "cluster_rat_RNA2ATAC", embedding = "UMAPX300")
ggAlignPlots(p1, p2, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b932cd8ef41-Date-2022-12-05_Time-09-30-16.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b932cd8ef41-Date-2022-12-05_Time-09-30-16.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b934490977-Date-2022-12-05_Time-09-30-16.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b934490977-Date-2022-12-05_Time-09-30-16.log
In [23]:
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "cluster_macaque", embedding = "UMAPX300")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "cluster_rat_RNA2ATAC", embedding = "UMAPX300")
ggAlignPlots(p1, p2, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b932c0ad52a-Date-2022-12-05_Time-09-30-21.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b932c0ad52a-Date-2022-12-05_Time-09-30-21.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-25b9363267f89-Date-2022-12-05_Time-09-30-21.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-25b9363267f89-Date-2022-12-05_Time-09-30-21.log
In [24]:
idxSample <- BiocGenerics::which(proj$Celltype2 %ni% c('Drop'))
cellsSample <- proj$cellNames[idxSample]
proj = proj[cellsSample, ]
proj = saveArchRProject(ArchRProj = proj)
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
In [ ]: